Biochemistry Commons^™

Discovery And Characterization Of Small Molecule Inhibitors Of Bromodomains, Md Rezaul Karim

USF Tampa Graduate Theses and Dissertations

The epigenetic “reader” modules bromodomains (BRDs) exert their diverse cellular functions through the recognition of acetylated lysines on histones and other proteins. Small molecule inhibitors of bromodomains have emerged as a promising therapeutic strategy to treat atherosclerotic cardiovascular diseases and cancers. Therefore, a large number of small molecule bromodomain inhibitors have been developed in the last decade, some of which are currently being assessed in the clinic. However, the success of bromodomain inhibitors is currently limited to the bromodomain and extra-terminal domain (BET) subfamily.

To address these, bromodomains outside the BET subfamily (non-BETs) such as TAF1, BRD7/9, TRIM28, and BRD8 …

In Vivo Biosynthesis Of Inorganic Nanomaterials Using Eukaryotes - A Review, Ashiqur Rahman, Julia Lin, Francisco E. Jaramillo, Dennis A. Bazylinski, Clayton Jeffryes, Si Amar Dahoumane

Life Sciences Faculty Research

Bionanotechnology, the use of biological resources to produce novel, valuable nanomaterials, has witnessed tremendous developments over the past two decades. This eco-friendly and sustainable approach enables the synthesis of numerous, diverse types of useful nanomaterials for many medical, commercial, and scientific applications. Countless reviews describing the biosynthesis of nanomaterials have been published. However, to the best of our knowledge, no review has been exclusively focused on the in vivo biosynthesis of inorganic nanomaterials. Therefore, the present review is dedicated to filling this gap by describing the many different facets of the in vivo biosynthesis of nanoparticles (NPs) using living eukaryotic …

Profiling The Circulating Mrna Transcriptome In Human Liver Disease, Aejaz Sayeed, Brielle E Dalvano, David E Kaplan, Usha Viswanathan, John Kulp, Alhaji H Janneh, Lu-Yu Hwang, Adam Ertel, Cataldo Doria, Timothy Block

Department of Cancer Biology Faculty Papers

The human circulation contains cell-free DNA and non-coding microRNA (miRNA). Less is known about the presence of messenger RNA (mRNA). This report profiles the human circulating mRNA transcriptome in people with liver cirrhosis (LC) and hepatocellular carcinoma (HCC) to determine whether mRNA analytes can be used as biomarkers of liver disease. Using RNAseq and RT-qPCR, we investigate circulating mRNA in plasma from HCC and LC patients and demonstrate detection of transcripts representing more than 19,000 different protein coding genes. Remarkably, the circulating mRNA expression levels were similar from person to person over the 21 individuals whose samples were analyzed by …

Translational Regulation Of Environmental Adaptation In Bacteria, Rodney Tollerson Ii, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bacteria must rapidly respond to both intracellular and environmental changes to survive. One critical mechanism to rapidly detect and adapt to changes in environmental conditions is control of gene expression at the level of protein synthesis. At each of the three major steps of translation—initiation, elongation, and termination—cells use stimuli to tune translation rate and cellular protein concentrations. For example, changes in nutrient concentrations in the cell can lead to translational responses involving mechanisms such as dynamic folding of riboswitches during translation initiation or the synthesis of alarmones, which drastically alter cell physiology. Moreover, the cell can fine-tune the levels …

The Kinetic Signatures Of Antibody Binding To M. Genitalium Adhesin Protein Fragments, Margaret C. Lunn

Honors Projects

Mycoplasma genitalium is a sexually-transmitted bacterial pathogen that persists in patients by adherence to cells through matrix glycoproteins and evasion of host antibodies. The MgpB and MgpC adherence proteins consist of variable and conserved regions. Variable regions undergo antigenic variation to avoid specific antibodies. However, the C-terminus (MgpB-4a) does not vary, is highly immunogenic, and antibodies to this region inhibit attachment and promote bacterial killing in vitro. To better understand how M. genitalium avoids clearance by antibodies to MgpB-4a in vivo we used surface plasmon resonance (SPR) to measure kinetic values of binding events. Binding of polyclonal rabbit antibodies (3935 …

A Highly Elastic And Fatigue-Resistant Natural Protein-Reinforced Hydrogel Electrolyte For Reversible-Compressible Quasi-Solid-State Supercapacitors, Jingya Nan, Gaitong Zhang, Tianyu Zhu, Zhongkai Wang, Lijun Wang, Hongsheng Wang, Fuxiang Chu, Chunpeng Wang, Chuanbing Tang

Faculty Publications

Compressible solid-state supercapacitors are emerging as promising power sources for next-generation flexible electronics with enhanced safety and mechanical integrity. Highly elastic and compressible solid electrolytes are in great demand to achieve reversible compressibility and excellent capacitive stability of these supercapacitor devices. Here, a lithium ion-conducting hydrogel electrolyte by integrating natural protein nanoparticles into polyacrylamide network is reported. Due to the synergistic effect of natural protein nanoparticles and polyacrylamide chains, the obtained hydrogel shows remarkable elasticity, high compressibility, and fatigue resistance properties. More significantly, the supercapacitor device based on this hydrogel electrolyte exhibits reversible compressibility under multiple cyclic compressions, working well …

Insights Into Desiccation Tolerance: Properties Of Late Embryogenesis Abundant Proteins From Embryos Of Artemia Franciscana, Blase Matthew Leblanc

LSU Doctoral Dissertations

LEA proteins are a family of intrinsically disordered proteins that are expressed in various life stages of anhydrobiotic organisms and have been strongly associated with survival during water stress. The brine shrimp Artemia franciscana is the only known anhydrobiotic animal that expresses LEA proteins from Groups 1, 3, and 6. Here, I report that AfrLEA6, a novel Group 6 LEA protein, is most highly expressed in embryos during diapause and decreases throughout pre-emergence development. Notably, there is an acute drop in expression upon termination of the diapause state and the titer of AfrLEA6 during diapause is 10-fold lower than values …

Evidence Of Pathogen-Induced Immunogenetic Selection Across The Large Geographic Range Of A Wild Seabird, Hila Levy, Stephen R. Fiddaman, Julianna A. Vianna, Daly Noll, Gemma Clucas, Jasmine K. H. Sidhu, Michael J. Polito, Charles A. Bost, Richard A. Phillips, Sarah Crofts, Gary D. Miller, Pierre Pistorius, Francesco Bonnadonna, Celine Le Bohec, Andres Barbosa, Phil Trathan, Andrea Raya Rey, Laurent A. F. Frantz, Tom Hart, Adrian L. Smith

Faculty Publications

Over evolutionary time, pathogen challenge shapes the immunepheno type of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between ''different clades. Inthis study, we examine the …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Dna Damage Recognition And Uvrb Loading By Uvra Within The Nucleotide Excision Repair Pathway, Silas Hartley

Dissertations, Theses, and Capstone Projects

Maintaining the cellular genome is paramount to survival by any organism. A mutated genome can have detrimental effects on different cellular processes, especially replication and transcription. Cells maintain their genome using different deoxyribonucleic acid (DNA) repair pathways. The nucleotide excision repair (NER) pathway has a unique capability of repairing the genome from several different mutations, deletions, and adducts. In bacteria, the NER pathway accomplishes repair through four important steps: damage recognition by UvrA, damage verification by UvrB, DNA incision by UvrC, and repair synthesis using various cellular machinery.

UvrA forms a head-to-head dimer (UvrA₂) with two ATPase sites …

Development Of Ligand Guided Selection (Ligs) To Identify Specific Dna Aptamers Against Cell Surface Proteins, Hasan Ekrem Zumrut

Dissertations, Theses, and Capstone Projects

Oligonucleotide aptamers (nucleic acid-based affinity reagents) are an emerging class of synthetic molecules that display high affinity and specificity towards their targets. Aptamer molecules for a target of interest are obtained using a combinatorial chemistry-based method termed systematic evolution of ligands by exponential enrichment (SELEX). SELEX is an in vitro selection process in which a random oligonucleotide library is subjected to repeated cycles of target incubation, separation, and amplification until target-specific evolved sequences become prevalent in the library. Typically, SELEX is used against target molecules such as small molecules and proteins, in their purified state. However, aptamers selected against purified …

Role Of The Hyaluronan Receptor, Stabilin-2/Hare, In Health And Disease, Edward N. Harris, Erika Baker

Department of Biochemistry: Faculty Publications

Stabilin-2/HARE is the primary clearance receptor for circulating hyaluronan (HA), a polysaccharide found in the extracellular matrix (ECM) of metazoans. HA has many biological functions including joint lubrication, ocular turgor pressure, skin elasticity and hydration, cell motility, and intercellular signaling, among many others. The regulatory system for HA content in the tissues, lymphatics, and circulatory systems is due, in part, to Stabilin-2/HARE. The activity of this receptor was discovered about 40 years ago (early 1980s), cloned in the mid-1990s, and has been characterized since then. Here, we discuss the overall domain organization of this receptor and how it correlates to …

Expression Of Stress Related Genes Of Penaeus Varnamei In Biofloc Closed Breeding System, Truong An Nguyen

Student Works (2020-2029)

The Pacific shrimp Penaeus vannamei, which is also known as the whiteleg shrimp, is fast becoming a key species of shrimp farming worldwide since this species has been cultured widely in many countries, such as Mexico, America, especially in Southeast Asian countries including Thailand, Vietnam, and Malaysia. In addition, the shrimp aquaculture industry has applied many new cultural techniques, especially biofloc technology – which is an eco-friendly culture technique and has many advantages over other traditional methods, such as high productivity, the stable environment of the culture, and low levels of feed conversion. Unfortunately, for so many years, shrimp farming …

Toxicity Studies Of 1'-S-1'-Acetoxychavicol Acetate In Rat Model, Ali Abdalla Yasir Osman

Student Works (2020-2029)

Natural compounds are the main source of therapeutic molecules for various diseases in this era, and most of the current medicines are derived from plants, microorganisms or animals. Nevertheless, the safety profile of these natural compounds has to be confirmed prior to their medicinal use. 1'-S-1'-acetoxychavicol acetate (ACA), a type of phenylpropanoid extracted from Alpinia conchigera Griff., is one of the natural compounds being investigated for its potential therapeutic purposes. ACA was previously reported to reduce tumour volume in athymic mice at the effective dose of 1.56 mg/kg body weight intraperitoneally and induce apoptotic death of tumour cells through the …

Protonic Capacitor: Elucidating The Biological Significance Of Mitochondrial Cristae Formation, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

For decades, it was not entirely clear why mitochondria develop cristae? The work employing the transmembrane-electrostatic proton localization theory reported here has now provided a clear answer to this fundamental question. Surprisingly, the transmembrane-electrostatically localized proton concentration at a curved mitochondrial crista tip can be significantly higher than that at the relatively flat membrane plane regions where the proton-pumping respiratory supercomplexes are situated. The biological significance for mitochondrial cristae has now, for the first time, been elucidated at a protonic bioenergetics level: 1) The formation of cristae creates more mitochondrial inner membrane surface area and thus more protonic capacitance for …

Land Application Of Sewage Sludge: Physiological And Biochemical Response Of The Rio Grande Tomato, Nabil Charchar, Ali Elafri, Redwane Rais, Halassi Ismahen

Journal of Bioresource Management

Treated wastewater produces sewage sludge as a by-product that may have beneficial implications on agricultural practices. The effects of sludge amendments on growth, morphological and biochemical characteristics of the agro-industrial Tomato cultivar Rio Grande were observed. A pot culture experiment was carried out during 4 months (16 February 2019 to 18 June 2019), at an experimental green house in the locality of Salah Soufi, Guelma, north-eastern Algeria. There were significant differences between soil and sewage sludge samples. Total nitrogen (20.58 mg/kg) was more available in sewage sludge than in soil (N = 2.09 ± 0.3 mg/kg). In contrast, sludge …

Analysis And Exploration Of Novel Antibiotic-Producing Streptomyces Spp. In Spokane County, Washington, Kyle S. Kramer, Jenifer B. Walke Ph.D

2020 Symposium Posters

According to the Centers for Disease Control and Prevention, a US citizen is infected by an antibiotic-resistant pathogen every 11 seconds, and every 15 minutes, a patient dies as a result of these infections. Due to the increasing incidence of antibiotic-resistant pathogenic microbes, the study and exploration of novel antibiotics from novel environments are imperative as infectious diseases are the second leading cause of death in the United States. The purpose of this research is to investigate and analyze antibiotic-producing soil microbes in Spokane County, WA, with hopes of discovering novel antibiotic-producing microbes, specifically Streptomyces species, and explore some of …

Strong Temporal Variability In Methane Fluxes From Natural Gas Well Pad Soils, Seth N. Lyman, Huy N. Q. Tran, Marc L. Mansfield, Ric Bowers, Ann Smith

Bingham Research Center

We measured methane and carbon dioxide fluxes at natural gas well pad soils and undisturbed soils in the Rocky Mountain and Gulf Coast regions of the United States, including producing and gas storage wells. We collected both short-term (15 min) and multi-day (between 3 and 8), continuous measurements at 47 well pads and two undisturbed locations. Methane fluxes varied by more than an order of magnitude over periods as short as 30 min (e.g., 19–593 mg m⁻² h⁻¹ in one instance), and diurnal and seasonal variability was also significant (e.g., spring-to-fall change from 509 to 14174 mg m …

A Study On The Regulation Of Mitochondrial Biogenesis And Gluconeogenesis In S. Cerevisiae, Manika Bhondeley

LSU New Orleans Theses and Dissertations

Budding yeast has been used as a powerful model organism to study the network that communicate functions of nucleus, cytoplasm and mitochondria. Depending upon environmental cues, yeast cells regulate their metabolic programming, for example, presence of glucose repress utilization of alternate carbon source to produce energy. This phenomenon is called carbon catabolite repression, which is relieved when glucose is limiting, and alternate carbon source utilization is achieved by an increase in mitochondrial biogenesis (oxidative catabolism) and the upregulation of TCA cycle and gluconeogenesis. Most of genes involved in alternate carbon source utilization are encoded in the nucleus and undergo tight …

The Role Of Redox Chemistry Of Disulfide Bonds In Cysteine Residues Of Membrane Proteins By Cuprous And Cupric Ions In Cell Death Of E. Coli, Morgan R. Stewart

University Honors Theses

The antimicrobial properties of copper have been thoroughly researched, but is still unclear what the actual mechanism of cell death is. This study explores the theory that copper ions and other copper sources act as an antibiotic for E. coli by cleaving the disulfide bonds of membrane proteins through redox chemistry, disrupting the cell membrane and causing cell death. The focus of this study is Cu(I) and Cu(II) interactions with the thiol containing amino acid, cysteine, and how these interactions may be responsible for copper’s toxicity. Cuprous ions have been found to be more toxic to E.coli than cupric …